Since I've got a pretty sweet SR app for my new phone that, among other things, can store characters created in Chummer, I figured I'd actually download the program and play around with it. Only thing is, the character I wanted to run through Chummer has a PQ from Augmentation, namely Bio-Compatability (Cyberware), which isn't in Chummer at all. Is there some sort of patch to add extra qualities in, or am I just going to have to work around this?

First, the thread should be in Community Projects.

That said, make sure that you've got the Augmentation book enabled through the Options menu (you'll need to restart Chummer if you had to enable any books). The Positive Quality is otherwise already in the program and automatically recalculates Essence loss from cyberware.

Are we talking the original Chummer for SR4 or Chummer 5? If he just recently downloaded Chummer it may be the version for 5e in which case he would not have access to Bio-Compatability as it hasn't been presented is SR5 yet.

I would guess it is the SR4 version since his character has Biocompatability. It sounds like he wants to build the character in Chummer so he can use an app on his phone to read the character. I would guess that app is Mobile Runner, which can read SR4 version Chummer files.
If this is the case, then Spellbinder has it right, make sure Augmentation (and any other source books you use) are checked in the option menu.

Normally I would agree with you Mantis. However he has a character that he want's to run through Chummer (he has not yet) but cannot because a +Q is missing. I read that to mean he hasn't really used Chummer before and when he wanted to put in a character found that the +Q was missing. Either he just never ran this 4e character through or he has never tried Chummer until recently (and probably after Chummer 5 came out).

I am not sure, but that is how I read it.

That got it, thank you. Also, yes, I'm using Chummer for 4th ed. I'm not currently planning on picking up SR5 do to it's apparent 'obvious beta'-ness.